PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

Browse

Filters

2015 - 201932020 - 202524

Settings

Scopus Q: search.filters.scopusQuartile.Q3WoS Q: search.filters.wosQuartile.Q3

Search Results

Now showing 1 - 10 of 27
  • Article
    Thermal Stresses in SOFC Stacks: The Role of Mismatch Among Thermal Conductivity of Adjacent Components
    (Tubitak Scientific & Technological Research Council Turkey, 2021-06-30) Aydin, Ozgur; Matsumoto, Go; Shiratori, Yusuke
    Generating power from renewable biogas in solid oxide fuel cells (SOFCs) is an environment-friendly, efficient, and promising energy conversion process. Biogas can be used in SOFCs via a reforming process for which dry reforming is more suitable as the reforming agent exists in the biogas mixture. Biogas can be directly reformed to H-2 -rich fuel stream in the anode chamber of a SOFC by the heat released during power generation. Exploiting the heat and water produced in the SOFC for internal reforming of biogas makes the energy conversion process very efficient; however, various challenges are reported. Thus, indirect internal reforming is opted for which a separate reforming domain is required. In an indirect internal reformer operating at usual conditions, dry reforming rate is quite high in the inlet and it decreases steeply toward the fuel outlet. Great temperature gradients develop over the reformer, since the dry reforming reaction is strongly endothermic. The abruptly varying rate of the reforming reaction affects the temperature fields in the adjacent components of SOFC and hence intolerable thermal stresses emerge on the SOFC components. In our preceding study, we graded the reforming domain, homogenized the temperature profile over the reforming domain, and executed performance and durability experiments. However, most of the experiments failed due to fracturing SOFC components hinting at existence of thermal stresses. In that study, we focused on minimizing the temperature gradients within the reforming domain; namely, we neglected the other processes. To eliminate the thermal stresses, we modeled the entire module of SOFC equipped with a reformer featuring a graded reforming domain. We found that the mismatch between the thermal conductivities of the adjacent module components is the major reason for the thermal stresses. When the mismatch is eliminated, thermal stresses disappear even if the reforming domain is not graded.
  • Article
    Citation - WoS: 6
    Citation - Scopus: 7
    Therapeutic Potential of Nitrogen-Substituted Oleanolic Acid Derivatives in Neuroinflammatory and Cytokine Pathways: Insights From Cell-Based and Computational Models
    (Wiley-VCH Verlag GmbH, 2025-04-22) Turgut, Gurbet Celik; Pepe, Nihan Aktas; Ekiz, Yagmur Ceylan; Senol, Halil; Sen, Alaattin
    This study was conducted to investigate the mechanism of the potential and anti-inflammatory properties of nitrogen-substituted oleanolic acid derivatives that can be used to treat neuroinflammatory diseases. Nitrogen-containing oleanolic acid derivatives have been evaluated for their anti-neuroinflammatory effects in vitro in neuronal and monocytic cell lines at nontoxic doses, and the production of cytokines (TNF-alpha, IL-6 and IL-17), the inflammatory enzyme induced nitric oxide synthase (iNOS) and NF-kappa B signalling under LPS-stimulated conditions, and the expression of genes associated with Alzheimer's disease have been assessed. In addition, molecular docking and molecular dynamics simulation assessments are conducted in silico. Key protein markers of neurodegenerative diseases, especially Alzheimer's disease and neuroinflammation, TAU protein levels, and microglial activation, as well as ionised calcium-binding adaptor protein-1 (IBA1) levels, were significantly reduced with the addition of oleanolic acid derivatives. LPS-induced NF-kappa B luciferase reporter activity and iNOS activity were significantly inhibited, approaching the levels in uninduced controls. The mRNA expression of proinflammatory cytokines critical for neuroinflammation, such as TNF-alpha, NF-kappa B, IL-6 and IL-17, was reduced twofold to sevenfold. Furthermore, the molecular docking and MD simulation analyses revealed potential interactions with the TNF-alpha and NF-kappa B proteins. These findings underscore the potential of oleanolic acid derivatives, particularly compound 16, as candidates for further development as therapeutic agents for neurodegenerative diseases associated with chronic inflammation.
  • Article
    Theoretical Investigation of Steric Effects on the S1 Potential Energy Surface of O-Carborane Derivatives
    (Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Alkan, Fahri
    TDDFT scan calculations were performed for s-carborane-anthracene derivatives (o-CB-X-Ant where X=-H,-CH3,-C2H5 and tert-butyl or-tBu) in order to understand the interplay between the steric effects, S1 potential energy surface (PES) and photophysical properties. The results show that all systems exhibit three local minima on the S1 PES, which correspond to the emissive LE and TICT state, along with the nonemissive CT state respectively. In the case of the unsubstituted system (o-CB-H-Ant), and-CH3 and-C2H5 substituted cases, S1 PES is predicted to be quite flat for certain conformations indicating that it is possible for these systems to reach the nonemissive CT state without a large energy penalty. In comparison, conformational pathways for the nonemissive CT state are predicted to be energetically unfavorable for o-CB-tBu-Ant as a result of both steric and electronic effects. These results provide a mechanism for the enhanced emission of cr-CB-fluorophore molecules with bulky ligands.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Theoretical Investigation of Substituent Effects on the Relative Stabilities and Electronic Structure of [BnXn]2- Clusters
    (Springer, 2021-11-29) Tahaoglu, Duygu; Alkan, Fahri; Durandurdu, Murat
    In this study, we provide a theoretical evaluation of relative stabilities and electronic structure for [BnXn](2-) clusters (n = 10, 12, 13, 14, 15, 16). Structural and electronic characteristics of [BnXn](2-) clusters are examined by comparison with the [B12X12](2-) counterparts with a focus on the substituent effects (X = H, F, Cl, Br, CN, BO, OH, NH2) on the electronic structure, electron detachment energies, formation enthalpies, and charge distributions. For the electronic structure and electron detachment energies, substituent effects on boron clusters are shown to follow a very similar trend to the mesomeric and inductive effects (+/- M and +/- I) of pi-conjugated systems, and the most stable derivatives in terms of HOMO/LUMO and electron detachment energies are calculated for CN and BO substituents due to strong -M effects. In the case of formation enthalpies for larger boron clusters (n >= 13), the icosahedral barrier is shown to increase with the halogen and CN substitution, whereas it is possible to reduce the icosahedral barrier for the cases of X = OH and NH2. It is shown that this reduction results from destabilizing the [B12X12](2-) cluster with electronic (+ M) and symmetry effects induced by OH and NH2 ligands.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    The Impact of COVID-19 on Healthcare Utilization in Turkey
    (Elsevier, 2024-09) Ugur, Zeynep B.; Durak, Aysenur
    Objectives: This study investigates the impact of the COVID-19 pandemic on healthcare utilization in Turkey. Methods: We utilized individual-level data derived from Turkish Statistical Institute 's annual surveys between 2014 and 2022 and estimated probit regression models. Results: We find that COVID-19 pandemic reduced healthcare utilization by 11.8% after taking into account a large set of background variables. Although our study finds that the elderly and those with health problems are more likely to use healthcare services under normal circumstances, the COVID-19 pandemic has caused notable drops in the healthcare utilization among the elderly (-6.5%) and those with health problems (-3.8%). Although those without health insurance had lower utilization of healthcare services before the pandemic, during the pandemic they were not particularly hit. Conclusion: We conclude that the pandemic did not lower the healthcare utilization in Turkey because of the supply constraints. Also, the evidence points to the reduced demand due to the fear of contagion rather than financial concerns.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 4
    Rapamycin and Niacin Combination Induces Apoptosis and Cell Cycle Arrest Through Autophagy Activation on Acute Myeloid Leukemia Cells
    (Springer, 2024-12-23) Subay, Lale Beril; Akcok, Emel Basak Gencer; Akcok, Ismail; Gencer Akçok, Emel Başak
    BackgroundAcute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by disorders in stem cell differentiation and excessive proliferation resulting in clonal expansion of dysfunctional cells called myeloid blasts. The combination of chemotherapeutic agents with natural product-based molecules is promising in the treatment of AML. In this study, we aim to investigate the anti-cancer effect of Rapamycin and Niacin combination on THP-1 and NB4 AML cell lines.Methods and ResultsThe anti-proliferative effects of Rapamycin and Niacin were determined by MTT cell viability assay in a dose- and time-dependent manner. The combination indexes were calculated by isobologram analysis. Furthermore, apoptosis was investigated by Annexin-V/Propidium Iodide(PI) double staining and cell cycle distribution was measured by PI staining. The expression levels of autophagy-related proteins were detected by western blotting. The combination of Rapamycin and Niacin synergistically decreased cell viability of AML cell lines. The combination treatment induced the apoptotic cell population of THP-1 and NB4 by 4.9-fold and 7.3-fold, respectively. In THP-1 cells, the cell cycle was arrested at the G2/M phase by 10% whereas the NB4 cells were accumulated at the G0/G1 phase. The combination treatment decreased Akt and p-Akt expression. Besides, the ATG7 expression was reduced by combination treatment on THP-1 cells. Similarly, the ATG5 level was downregulated in NB4 cells. The level of LC3B-II/LC3B-I, which is an indicator of autophagy flux, was upregulated in THP-1 and NB4 cells.ConclusionAlthough further studies are required, the combination of Rapamycin and Niacin combats cell proliferation by inducing cellular apoptosis, cell cycle arrest and autophagy activation.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 4
    Prediction of Biomechanical Properties of Ex Vivo Human Femoral Cortical Bone Using Raman Spectroscopy and Machine Learning Algorithms
    (Elsevier, 2025-09) Unal, Mustafa; Unlu, Ramazan; Uppuganti, Sasidhar; Nyman, Jeffry S.
    This study applied Raman spectroscopy (RS) to ex vivo human cadaveric femoral mid-diaphysis cortical bone specimens (n = 118 donors; age range 21-101 years) to predict fracture toughness properties via machine learning (ML) models. Spectral features, together with demographic variables (age, sex) and structural parameters (cortical porosity, volumetric bone mineral density), were fed into support vector regression (SVR), extreme tree regression (ETR), extreme gradient boosting (XGB), and ensemble models to predict fracture-toughness metrics such as crack-initiation toughness (Kinit) and energy-to-fracture (J-integral). Feature selection was based on Raman-derived mineral and organic matrix parameters, such as nu 1Phosphate (PO4)/CH2-wag, nu 1PO4/ Amide I, and others, to capture the complex composition of bone. Our results indicate that ensemble models consistently outperformed individual models, with the best performance for crack initiation toughness (Kinit) prediction being achieved using the ensemble approach. This yielded a coefficient of determination (R2) of 0.623, root-mean squared error (RMSE) of 1.320, mean absolute error (MAE) of 1.015, and mean percentage absolute error (MAPE) of 0.134. For prediction of the overall energy to propagate a crack (J-integral), the XGB model achieved an R2 of 0.737, RMSE of 2.634, MAE of 2.283, and MAPE of 0.240. This study highlights the importance of incorporating mineral quality properties (MP) and organic matrix properties (OMP) for enhanced prediction accuracy. This work represents the first-ever study combining Raman spectroscopy with other clinical and structural features to predict fracture toughness of human cortical bone, demonstrating the potential of artificial intelligence (AI) and ML in advancing bone research. Future studies could focus on larger datasets and more advanced modeling techniques to further improve predictive capabilities.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Possible Boron-Rich Amorphous Silicon Borides From Ab Initio Simulations
    (Springer, 2023-03-10) Karacaoglan, Aysegul Ozlem Cetin; Durandurdu, Murat
    ContextBy means of ab initio molecular dynamics simulations, possible boron-rich amorphous silicon borides (BnSi1-n, 0.5 <= n <= 0.95) are generated and their microstructure, electrical properties and mechanical characters are scrutinized in details. As expected, the mean coordination number of each species increases progressively and more closed packed structures form with increasing B concentration. In all amorphous models, pentagonal pyramid-like configurations are observed and some of which lead to the development of B-12 and B11Si icosahedrons. It should be noted that the B11Si icosahedron does not form in any crystalline silicon borides. Due to the affinity of B atoms to form cage-like clusters, phase separations (Si:B) are perceived in the most models. All simulated amorphous configurations are a semiconducting material on the basis of GGA+U calculations. The bulk modulus of the computer-generated amorphous compounds is in the range of 90 GPa to 182 GPa. As predictable, the Vickers hardness increases with increasing B content and reaches values of 25-33 GPa at 95% B concentration. Due to their electrical and mechanical properties, these materials might offer some practical applications in semiconductor technologies.MethodThe density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations were used to generate B-rich amorphous configurations.
  • Article
    Citation - Scopus: 1
    Possible Drug-Drug Interactions Between Mesalamine and Tricyclic Antidepressants Through CYP2D6 Metabolism - in Silico and in Vitro Analyses
    (Georg Thieme Verlag, 2025-04-01) Ozen, Melek B.; Gazioğlu, Işil; Ozgun-Acar, Özden; Guner, Hüseyin; Semiz, Gürkan; Sen, Alaattin; Ozgun Acar, Ozden
    Mesalamine (mesalazine, 5-aminosalicylic acid, 5-ASA) is an essential anti-inflammatory agent both used for therapy and as a remission control in patients with inflammatory bowel diseases (IBD) such as ulcerative colitis (UC). Tricyclic antidepressants (TCAs) are used to alleviate remaining symptoms in patients already receiving IBD therapy or with quiescent inflammation. The cytochrome P4502D6 enzyme is involved in the metabolism of TCAs. Hence, it is crucial to investigate the role of CYP2D6 in 5-ASA metabolism. Initially, in silico analysis involving the docking of 5-ASA to CYP2D6 and molecular dynamics simulations was conducted. Next, the rate of O-demethylation of a nonfluorescent probe 3-[2-(N,N-diethyl-N-methylammonium)-ethyl]-7-methoxy-4-methylcoumarin (AMMC) into a fluorescent metabolite AMHC (3-[2-(N,N-diethyl-N-methylammonium)ethyl]-7-hydroxy-4-methylcoumarin) was optimized with baculosomes co-expressing human CYP2D6 and human P450 oxidoreductase (hCPR) to monitor CYP2D6 activity in a microtiter plate assay. The apparent Km and Vmax were found to be 1.30 μM and 32.68 pmol/min/mg of protein for the O-demethylation of AMMC to AMHC, and the reaction was linear for 40 min. Then, nonselective inhibition of CYP2D6 activity with various concentrations of 5-ASA was detected. Finally, the conversion of AMMC to metabolites was analyzed by HPLC-ESI-MS/MS spectrometry, and none were identified. Thus, this study suggests that concurrent use of mesalamine with TCA may lead to adverse effects, and CYP2D6 genotyping should be routinely performed on these patients to eliminate possible threats. © 2025 Elsevier B.V., All rights reserved.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 3
    Multi Fragment Melting Analysis System (MFMAS) for One-Step Identification of Lactobacilli
    (Elsevier, 2020-10) Kesmen, Zulal; Kilic, Ozge; Gormez, Yasin; Celik, Mete; Bakir-Gungor, Burcu
    The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.